Contacts of the helix formed by residues 205 - 221 (chain D) in PDB entry 5MBV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 205 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ALA* 3.4 6.5 - - - +
204D PRO* 1.3 86.6 - - + +
206D GLY* 1.3 59.4 + - - +
207D LYS* 4.1 9.6 - - - +
208D ALA* 3.5 22.3 + - - +
209D ALA* 3.0 24.5 + - - +
239D THR* 4.6 2.9 - - - -
273D MET* 3.9 25.6 - - + +
494D PHE* 6.3 2.7 - - + -
495D ASN 5.1 10.1 - - - +
542D GLN 5.6 2.3 + - - +
543D GLY* 5.7 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D THR* 1.3 69.4 - - - +
207D LYS* 1.3 65.0 + - - +
209D ALA* 3.4 9.8 - - - +
210D ALA* 3.0 24.6 + - - +
239D THR* 3.9 18.4 + - - +
494D PHE* 5.1 17.3 - - - +
515D PRO* 5.6 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D THR* 3.2 8.9 - - - +
206D GLY* 1.3 78.0 - - - +
208D ALA* 1.3 64.0 + - - +
210D ALA* 3.2 4.4 + - - +
211D ARG* 3.1 19.0 + - + +
432D ILE* 6.1 3.2 - - - +
436D ASN* 4.5 18.5 - - - +
494D PHE* 6.0 0.6 - - - -
496D GLY 5.3 8.1 - - - +
497D ASP* 4.8 18.0 + - + +
498D ILE* 5.9 4.1 - - - +
543D GLY 4.8 10.3 - - - +
544D SER* 4.5 22.2 - - - +
545D GLU 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ALA* 4.2 7.9 - - + -
205D THR* 3.5 17.6 + - - +
207D LYS* 1.3 80.7 - - - +
209D ALA* 1.3 57.4 + - - +
211D ARG* 3.3 15.3 + - + +
212D LEU* 2.8 27.4 + - - +
269D ASP* 4.0 5.6 - - - +
270D GLU* 4.0 28.3 - - + -
273D MET* 5.0 0.9 - - + -
543D GLY* 4.6 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ALA* 3.7 15.0 - - + +
205D THR 3.0 18.6 + - - +
206D GLY* 3.4 12.3 - - - +
207D LYS 3.1 0.4 - - - -
208D ALA* 1.3 75.9 - - - +
210D ALA* 1.3 57.7 + - - +
212D LEU* 2.9 20.1 + - - +
213D THR* 3.0 20.8 + - - +
237D ALA* 3.8 26.1 - - + +
238D SER* 4.6 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D GLY 3.0 16.1 + - - +
207D LYS* 3.8 3.6 - - - +
209D ALA* 1.3 75.1 - - - +
211D ARG* 1.3 61.2 + - - +
213D THR* 2.9 23.8 + - - +
214D GLU* 3.3 14.9 + - - +
515D PRO* 4.8 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D PRO* 5.2 12.7 - - - +
174D GLY 5.8 1.8 - - - +
177D LYS* 5.8 3.4 - - - +
207D LYS* 3.1 14.0 + - + +
208D ALA* 3.4 15.5 - - - +
209D ALA 3.2 0.2 - - - -
210D ALA* 1.3 77.7 - - - +
212D LEU* 1.3 58.4 + - - +
214D GLU* 4.6 4.2 - - - +
215D SER* 2.8 38.4 + - - +
269D ASP* 5.6 3.8 - - - +
270D GLU* 4.1 19.1 + - - +
543D GLY* 3.3 32.3 + - - -
544D SER 4.8 1.2 + - - -
545D GLU* 2.8 39.5 + - - +
572D ARG* 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D THR* 4.7 11.2 - - + +
201D LEU* 3.8 27.8 - - + -
202D ALA 4.2 11.9 - - - +
208D ALA 2.8 13.4 + - - +
209D ALA* 2.9 10.7 + - - +
211D ARG* 1.3 77.6 - - - +
213D THR* 1.3 59.9 + - - +
215D SER* 4.8 1.1 - - - -
216D LEU* 2.8 62.0 + - + +
237D ALA* 4.6 3.1 - - + -
267D VAL* 4.7 5.8 - - + +
269D ASP* 3.6 40.8 - - + +
295D LEU* 4.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D LEU* 4.7 7.4 - - + -
209D ALA 3.3 13.0 - - - +
210D ALA* 2.9 16.7 + - - +
212D LEU* 1.3 77.7 - - - +
214D GLU* 1.3 60.2 + - - +
216D LEU* 3.9 2.9 - - - +
217D GLY* 2.9 24.8 + - - -
235D GLU 5.1 1.6 - - - -
236D ASP* 3.9 23.1 + - + +
237D ALA* 3.2 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ALA 3.3 12.7 + - - +
211D ARG* 4.6 3.9 - - - +
213D THR* 1.3 81.4 + - - +
215D SER* 1.3 65.0 + - - +
217D GLY* 3.1 2.4 + - - -
218D LYS* 3.0 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D THR* 3.5 31.0 - - - +
211D ARG* 2.8 32.3 + - - +
212D LEU* 4.2 1.6 - - - -
214D GLU* 1.3 78.4 - - - +
216D LEU* 1.3 62.5 + - - +
218D LYS* 3.4 7.3 + - - +
219D ALA* 3.2 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D THR* 3.6 28.7 - - + +
181D VAL* 4.0 20.9 - - + -
182D ALA* 4.2 9.4 - - + +
185D LEU* 4.5 10.8 - - + -
201D LEU* 3.7 39.9 - - + -
212D LEU* 2.8 43.0 + - + +
213D THR* 4.1 3.6 - - - +
215D SER* 1.3 76.9 - - - +
217D GLY* 1.3 57.3 + - - +
219D ALA* 4.0 1.6 - - - +
220D LEU* 3.1 41.6 + - + +
234D PRO* 5.7 0.7 - - + -
267D VAL* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D THR 2.9 16.2 + - - -
214D GLU* 3.1 4.2 + - - -
216D LEU* 1.3 78.1 - - - +
218D LYS* 1.3 63.1 + - - +
220D LEU* 4.1 4.1 - - - +
221D ARG* 3.2 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D GLU* 3.0 37.6 + - + +
215D SER* 4.0 6.3 - - - +
216D LEU 3.4 0.2 - - - -
217D GLY* 1.3 77.4 - - - +
219D ALA* 1.3 61.1 + - - +
220D LEU 3.7 0.2 + - - -
221D ARG* 3.8 9.7 + - + +
222D GLN* 3.8 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D THR* 4.4 2.9 - - + +
179D THR* 4.1 27.9 - - + +
182D ALA* 3.6 25.6 - - + +
183D LYS* 5.6 5.0 - - - -
215D SER 3.2 17.1 + - - +
216D LEU* 4.1 1.3 - - - +
218D LYS* 1.3 78.7 - - - +
220D LEU* 1.3 61.8 + - - +
221D ARG 3.4 0.2 - - - -
222D GLN* 3.4 22.7 + - - +
223D LEU* 4.3 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D ALA* 3.7 34.1 - - + +
185D LEU* 5.0 13.7 - - + -
186D ALA* 4.4 15.9 - - + +
189D ILE* 6.6 0.4 - - + -
216D LEU* 3.1 27.6 + - + +
217D GLY* 4.2 4.7 - - - +
218D LYS 3.4 0.2 - - - -
219D ALA* 1.3 73.7 - - - +
221D ARG* 1.3 64.4 + - + +
222D GLN 3.1 5.4 - - - -
223D LEU* 3.3 25.5 + - + +
225D LEU* 5.0 14.4 - - + +
233D ILE* 4.1 37.6 - - + +
234D PRO* 5.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D GLY* 3.2 20.0 + - - +
218D LYS* 3.8 6.3 + - - +
219D ALA 3.4 0.4 - - - -
220D LEU* 1.3 79.9 - - + +
222D GLN* 1.3 57.4 + - - +
223D LEU 3.2 7.0 + - - +
230D LYS* 3.5 34.4 + - - +
233D ILE* 4.7 16.5 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il